Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100522 |
| Name | oriT_pBHB  |
| Organism | Comamonas sp. 7D-2 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_021077 (90209..90581 [-], 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_pBHB
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCACCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCACCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 593 | GenBank | YP_007878472 |
| Name | TraI_pBHB |
UniProt ID | M9V0P4 |
| 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_007878472.1 TraI (plasmid) [Comamonas sp. 7D-2]
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 | M9V0P4 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 107375..118052
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTC95_RS00525 (K936_p037) | 102999..103850 | + | 852 | WP_011296189 | recombinase family protein | - |
| HTC95_RS00530 (K936_p113) | 103852..104610 | - | 759 | WP_012805979 | hypothetical protein | - |
| HTC95_RS00535 (K936_p046) | 104681..105112 | - | 432 | WP_001665065 | OmpA family protein | - |
| HTC95_RS00540 (K936_p045) | 105128..105826 | - | 699 | WP_011114053 | TraX family protein | - |
| HTC95_RS00545 (K936_p044) | 105826..106092 | - | 267 | WP_010890140 | hypothetical protein | - |
| HTC95_RS00550 (K936_p043) | 106121..106756 | - | 636 | WP_011114052 | transglycosylase SLT domain-containing protein | - |
| HTC95_RS00555 (K936_p042) | 106770..107357 | - | 588 | WP_010890138 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HTC95_RS00560 (K936_p041) | 107375..109093 | - | 1719 | WP_011114051 | P-type conjugative transfer protein TrbL | virB6 |
| HTC95_RS00565 (K936_p040) | 109104..109331 | - | 228 | WP_000644148 | entry exclusion lipoprotein TrbK | - |
| HTC95_RS00570 (K936_p039) | 109341..110105 | - | 765 | WP_010890135 | P-type conjugative transfer protein TrbJ | virB5 |
| HTC95_RS00575 (K936_p038) | 110126..111547 | - | 1422 | WP_011114050 | TrbI/VirB10 family protein | virB10 |
| HTC95_RS00580 (K936_p114) | 111552..112040 | - | 489 | WP_006122479 | conjugal transfer protein TrbH | - |
| HTC95_RS00585 (K936_p115) | 112043..112942 | - | 900 | WP_006122480 | P-type conjugative transfer protein TrbG | virB9 |
| HTC95_RS00590 (K936_p116) | 112960..113742 | - | 783 | WP_011114048 | conjugal transfer protein TrbF | virB8 |
| HTC95_RS00595 (K936_p117) | 113739..116297 | - | 2559 | WP_011114047 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HTC95_RS00600 (K936_p118) | 116294..116605 | - | 312 | WP_001207961 | conjugal transfer protein TrbD | virB3 |
| HTC95_RS00605 (K936_p119) | 116609..117073 | - | 465 | WP_011114046 | conjugal transfer system pilin TrbC | virB2 |
| HTC95_RS00610 (K936_p120) | 117090..118052 | - | 963 | WP_000132020 | P-type conjugative transfer ATPase TrbB | virB11 |
| HTC95_RS00615 (K936_p121) | 118362..118724 | - | 363 | WP_011114045 | transcriptional regulator | - |
| HTC95_RS00620 (K936_p122) | 118838..119179 | + | 342 | WP_000019167 | single-stranded DNA-binding protein | - |
Host bacterium
| ID | 983 | GenBank | NC_021077 |
| Plasmid name | pBHB | Incompatibility group | IncP1 |
| Plasmid size | 119225 bp | Coordinate of oriT [Strand] | 90209..90581 [-] |
| Host baterium | Comamonas sp. 7D-2 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | merR, merT, merP, merA, merD, merE |
| Degradation gene | p-nitrobenzoate degradation |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIF24 |