Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100494 |
| Name | oriT_pDB1  |
| Organism | Variovorax sp. DB1 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019320 (63295..63667 [+], 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_pDB1
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 565 | GenBank | YP_006963148 |
| Name | TraI_pDB1 |
UniProt ID | I3RYJ8 |
| Length | 746 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 746 a.a. Molecular weight: 82038.71 Da Isoelectric Point: 10.7900
>YP_006963148.1 conjugal transfer relaxase TraI (plasmid) [Variovorax sp. DB1]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
LQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
LQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | I3RYJ8 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 35824..46501
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS989_RS00180 (pDB1_0350) | 31702..32511 | + | 810 | WP_005800232 | IS21-like element helper ATPase IstB | - |
| HS989_RS00350 | 32707..32811 | - | 105 | Protein_36 | mercuric transporter MerT family protein | - |
| HS989_RS00190 (pDB1_0360) | 32883..33317 | + | 435 | WP_003131969 | mercury resistance transcriptional regulator MerR | - |
| HS989_RS00195 (pDB1_0370) | 33430..34650 | - | 1221 | WP_011114072 | plasmid replication initiator TrfA | - |
| HS989_RS00200 (pDB1_0380) | 34697..35038 | - | 342 | WP_000019167 | single-stranded DNA-binding protein | - |
| HS989_RS00205 (pDB1_0390) | 35152..35514 | + | 363 | WP_011114045 | transcriptional regulator | - |
| HS989_RS00210 (pDB1_0400) | 35824..36786 | + | 963 | WP_000132020 | P-type conjugative transfer ATPase TrbB | virB11 |
| HS989_RS00215 (pDB1_0410) | 36803..37267 | + | 465 | WP_011114046 | conjugal transfer system pilin TrbC | virB2 |
| HS989_RS00220 (pDB1_0420) | 37271..37582 | + | 312 | WP_001207961 | conjugal transfer protein TrbD | virB3 |
| HS989_RS00225 (pDB1_0430) | 37579..40137 | + | 2559 | WP_011114047 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HS989_RS00230 (pDB1_0440) | 40134..40916 | + | 783 | WP_011114048 | conjugal transfer protein TrbF | virB8 |
| HS989_RS00235 (pDB1_0450) | 40934..41833 | + | 900 | WP_006122480 | P-type conjugative transfer protein TrbG | virB9 |
| HS989_RS00240 (pDB1_0460) | 41836..42324 | + | 489 | WP_006122479 | conjugal transfer protein TrbH | - |
| HS989_RS00245 (pDB1_0470) | 42329..43750 | + | 1422 | WP_011114050 | TrbI/VirB10 family protein | virB10 |
| HS989_RS00250 (pDB1_0480) | 43771..44535 | + | 765 | WP_010890135 | P-type conjugative transfer protein TrbJ | virB5 |
| HS989_RS00255 (pDB1_0490) | 44545..44772 | + | 228 | WP_000644148 | entry exclusion lipoprotein TrbK | - |
| HS989_RS00260 (pDB1_0500) | 44783..46501 | + | 1719 | WP_011114051 | P-type conjugative transfer protein TrbL | virB6 |
| HS989_RS00265 (pDB1_0510) | 46519..47106 | + | 588 | WP_010890138 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HS989_RS00270 (pDB1_0520) | 47120..47755 | + | 636 | WP_011114052 | transglycosylase SLT domain-containing protein | - |
| HS989_RS00275 (pDB1_0530) | 47784..48050 | + | 267 | WP_010890140 | hypothetical protein | - |
| HS989_RS00280 (pDB1_0540) | 48050..48748 | + | 699 | WP_011114053 | TraX family protein | - |
| HS989_RS00285 (pDB1_0550) | 48764..49195 | + | 432 | WP_001665065 | OmpA family protein | - |
| HS989_RS00290 (pDB1_0560) | 49350..50024 | + | 675 | WP_011178411 | DNA methylase | - |
| HS989_RS00295 (pDB1_0570) | 50026..50877 | - | 852 | WP_011296189 | recombinase family protein | - |
Host bacterium
| ID | 955 | GenBank | NC_019320 |
| Plasmid name | pDB1 | Incompatibility group | IncP1 |
| Plasmid size | 65269 bp | Coordinate of oriT [Strand] | 63295..63667 [+] |
| Host baterium | Variovorax sp. DB1 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIF24 |