Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 116398 |
| Name | oriT_pBP136Km  |
| Organism | Bordetella pertussis |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OR146256 (29881..29979 [+], 99 nt) |
| oriT length | 99 nt |
| IRs (inverted repeats) | 71..77, 79..85 (GGCGTTA..TAACGCC) 24..31, 34..41 (TAACCGGC..GCCGGTTA) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 99 nt
>oriT_pBP136Km
GAATAAGGGGAAGCGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCGCCCATCTTGCCCGCCTTACGGCGTTAATAACGCCAAGGAAAGTCTACA
GAATAAGGGGAAGCGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCGCCCATCTTGCCCGCCTTACGGCGTTAATAACGCCAAGGAAAGTCTACA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 10478 | GenBank | WP_011666401 |
| Name | traI_R7L28_RS00140_pBP136Km |
UniProt ID | Q08KX8 |
| Length | 745 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 745 a.a. Molecular weight: 82221.09 Da Isoelectric Point: 10.8818
>WP_011666401.1 TraI/MobA(P) family conjugative relaxase [Bordetella pertussis]
MILKHVPMRSLGKSDFAELANYITDAQSKEHRLGEVRLTNCHAATVGDAITEVLATQHTNTRATGDKTYH
LLVSFPPGENPPAAVLQQVEERVCAALGYSEHQRISAVHNDTDHLHIHIAINKIHPVRNTMHEPFQAYRT
MADIAVKLEKEFGLQQVNHSSKRTLAEGRAGDMEHHAGVESLVGWIRRECLDEITNAQTWQELHQVMREN
GLELRSRANGFVIEASDGTMVKASTVARDLSRPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYRADQQSLTTARGQALERARHRKNRLIEAAKRSHRLRRATIKVVGEGRTTKKLLYAQASKALRSE
IQAINKQFQQERAALYAEHSRRTWVDWLKKEAHHGNTEALAALRAREKAGLKGNTIRGEGQAKPGHAPAV
DNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVDS
QLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQWPLADQHATGAAAVARAGDGRPAA
GRGDRADAGIHAANVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQP
DHALRRAISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALAL
LKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR
MILKHVPMRSLGKSDFAELANYITDAQSKEHRLGEVRLTNCHAATVGDAITEVLATQHTNTRATGDKTYH
LLVSFPPGENPPAAVLQQVEERVCAALGYSEHQRISAVHNDTDHLHIHIAINKIHPVRNTMHEPFQAYRT
MADIAVKLEKEFGLQQVNHSSKRTLAEGRAGDMEHHAGVESLVGWIRRECLDEITNAQTWQELHQVMREN
GLELRSRANGFVIEASDGTMVKASTVARDLSRPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYRADQQSLTTARGQALERARHRKNRLIEAAKRSHRLRRATIKVVGEGRTTKKLLYAQASKALRSE
IQAINKQFQQERAALYAEHSRRTWVDWLKKEAHHGNTEALAALRAREKAGLKGNTIRGEGQAKPGHAPAV
DNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVDS
QLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQWPLADQHATGAAAVARAGDGRPAA
GRGDRADAGIHAANVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQP
DHALRRAISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALAL
LKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q08KX8 |
T4CP
| ID | 12229 | GenBank | WP_011666400 |
| Name | t4cp2_R7L28_RS00135_pBP136Km |
UniProt ID | _ |
| Length | 637 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 637 a.a. Molecular weight: 70086.35 Da Isoelectric Point: 8.4056
>WP_011666400.1 type IV secretory system conjugative DNA transfer family protein [Bordetella pertussis]
MKIKMNNAVGPQVRAAKPKPSKLLPVLGAASIVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNF
LEIVTGRAAPTATGVYVGGWQDKDGNFYYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWSPSCVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDEGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGPDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQAET
EGERITI
MKIKMNNAVGPQVRAAKPKPSKLLPVLGAASIVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNF
LEIVTGRAAPTATGVYVGGWQDKDGNFYYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWSPSCVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDEGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGPDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQAET
EGERITI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2401..12963
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| R7L28_RS00005 | 1..1224 | - | 1224 | WP_011666379 | plasmid replication initiator TrfA | - |
| R7L28_RS00010 | 1267..1605 | - | 339 | WP_011666380 | single-stranded DNA-binding protein | - |
| R7L28_RS00015 | 1719..2081 | + | 363 | WP_176451039 | transcriptional regulator | - |
| R7L28_RS00020 | 2401..3363 | + | 963 | WP_011666382 | P-type conjugative transfer ATPase TrbB | virB11 |
| R7L28_RS00025 | 3379..3843 | + | 465 | WP_011114046 | conjugal transfer system pilin TrbC | virB2 |
| R7L28_RS00030 | 3847..4158 | + | 312 | WP_001207961 | conjugal transfer protein TrbD | virB3 |
| R7L28_RS00035 | 4155..6713 | + | 2559 | WP_011666383 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| R7L28_RS00040 | 6710..7492 | + | 783 | WP_011666384 | conjugal transfer protein TrbF | virB8 |
| R7L28_RS00045 | 7510..8409 | + | 900 | WP_176451040 | P-type conjugative transfer protein TrbG | virB9 |
| R7L28_RS00050 | 8412..8876 | + | 465 | WP_011666386 | TrbH | - |
| R7L28_RS00055 | 8881..10293 | + | 1413 | WP_011666387 | TrbI/VirB10 family protein | virB10 |
| R7L28_RS00060 | 10314..11078 | + | 765 | WP_011666388 | P-type conjugative transfer protein TrbJ | virB5 |
| R7L28_RS00065 | 11088..11315 | + | 228 | WP_000644148 | entry exclusion lipoprotein TrbK | - |
| R7L28_RS00070 | 11326..12963 | + | 1638 | WP_317623545 | P-type conjugative transfer protein TrbL | virB6 |
| R7L28_RS00075 | 12981..13568 | + | 588 | WP_011666390 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| R7L28_RS00080 | 13582..14217 | + | 636 | WP_011666391 | transglycosylase SLT domain-containing protein | - |
| R7L28_RS00085 | 14246..14512 | + | 267 | WP_010890140 | hypothetical protein | - |
| R7L28_RS00090 | 14512..15210 | + | 699 | WP_011666392 | TraX family protein | - |
| R7L28_RS00095 | 15226..15657 | + | 432 | WP_011666393 | OmpA family protein | - |
| R7L28_RS00100 | 15812..16486 | + | 675 | WP_011666394 | hypothetical protein | - |
| R7L28_RS00105 | 16488..17339 | - | 852 | WP_011666395 | recombinase family protein | - |
| R7L28_RS00110 | 17449..17688 | + | 240 | WP_176451037 | hypothetical protein | - |
Host bacterium
| ID | 16831 | GenBank | NZ_OR146256 |
| Plasmid name | pBP136Km | Incompatibility group | IncP1 |
| Plasmid size | 42389 bp | Coordinate of oriT [Strand] | 29881..29979 [+] |
| Host baterium | Bordetella pertussis |
Cargo genes
| Drug resistance gene | aph(3')-Ia |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |