Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100267 |
| Name | oriT_pAMMD-1  |
| Organism | Burkholderia ambifaria AMMD |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_008385 (14483..14855 [-], 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_pAMMD-1
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAACCCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAACCCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 338 | GenBank | WP_011117146 |
| Name | TraI_pAMMD-1 |
UniProt ID | A0A1A5DBL5 |
| Length | 746 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 746 a.a. Molecular weight: 82120.82 Da Isoelectric Point: 10.8213
>WP_011117146.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWVKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQNLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHRRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWVKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQNLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHRRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A1A5DBL5 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 32885..43562
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| BAMB_RS32925 (Bamb_6618) | 29073..29453 | - | 381 | WP_011655359 | hypothetical protein | - |
| BAMB_RS32930 (Bamb_6619) | 29539..30036 | - | 498 | WP_011655360 | SAM-dependent methyltransferase | - |
| BAMB_RS32935 (Bamb_6620) | 30191..30622 | - | 432 | WP_001665065 | OmpA family protein | - |
| BAMB_RS32940 (Bamb_6621) | 30638..31336 | - | 699 | WP_011114053 | TraX family protein | - |
| BAMB_RS32945 (Bamb_6622) | 31336..31602 | - | 267 | WP_010890140 | hypothetical protein | - |
| BAMB_RS32950 (Bamb_6623) | 31631..32266 | - | 636 | WP_011114052 | transglycosylase SLT domain-containing protein | - |
| BAMB_RS32955 (Bamb_6624) | 32280..32867 | - | 588 | WP_010890138 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| BAMB_RS32960 (Bamb_6625) | 32885..34603 | - | 1719 | WP_011114051 | P-type conjugative transfer protein TrbL | virB6 |
| BAMB_RS32965 (Bamb_6626) | 34614..34841 | - | 228 | WP_000644148 | entry exclusion lipoprotein TrbK | - |
| BAMB_RS32970 (Bamb_6627) | 34851..35615 | - | 765 | WP_010890135 | P-type conjugative transfer protein TrbJ | virB5 |
| BAMB_RS32975 (Bamb_6628) | 35636..37057 | - | 1422 | WP_011114050 | TrbI/VirB10 family protein | virB10 |
| BAMB_RS32980 (Bamb_6629) | 37062..37550 | - | 489 | WP_006122479 | conjugal transfer protein TrbH | - |
| BAMB_RS32985 (Bamb_6630) | 37553..38452 | - | 900 | WP_006122480 | P-type conjugative transfer protein TrbG | virB9 |
| BAMB_RS32990 (Bamb_6631) | 38470..39252 | - | 783 | WP_006122481 | conjugal transfer protein TrbF | virB8 |
| BAMB_RS32995 (Bamb_6632) | 39249..41807 | - | 2559 | WP_011114047 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| BAMB_RS33000 (Bamb_6633) | 41804..42115 | - | 312 | WP_001207961 | conjugal transfer protein TrbD | virB3 |
| BAMB_RS33005 (Bamb_6634) | 42119..42583 | - | 465 | WP_011114046 | conjugal transfer system pilin TrbC | virB2 |
| BAMB_RS33010 (Bamb_6635) | 42600..43562 | - | 963 | WP_000132020 | P-type conjugative transfer ATPase TrbB | virB11 |
Host bacterium
| ID | 729 | GenBank | NC_008385 |
| Plasmid name | pAMMD-1 | Incompatibility group | IncP1 |
| Plasmid size | 43581 bp | Coordinate of oriT [Strand] | 14483..14855 [-] |
| Host baterium | Burkholderia ambifaria AMMD |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |