Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120099 |
| Name | oriT_pXAM48  |
| Organism | Xanthomonas phaseoli pv. manihotis strain CHN01 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP083579 (7080..7183 [-], 104 nt) |
| oriT length | 104 nt |
| IRs (inverted repeats) | 64..70, 73..79 (CACCGGC..GCCGGTG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 104 nt
>oriT_pXAM48
GCCTCGCAGAGCAGGATTCCCGTTGAGCGCCGAAGGCGCGAATAAGGGAGGGTGAAGAAGGAACACCGGCTTGCCGGTGGGCCTACTTCACATATCCTGCCCGG
GCCTCGCAGAGCAGGATTCCCGTTGAGCGCCGAAGGCGCGAATAAGGGAGGGTGAAGAAGGAACACCGGCTTGCCGGTGGGCCTACTTCACATATCCTGCCCGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12658 | GenBank | WP_229014497 |
| Name | traI_K9838_RS22665_pXAM48 |
UniProt ID | _ |
| Length | 831 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 831 a.a. Molecular weight: 90602.94 Da Isoelectric Point: 10.7026
>WP_229014497.1 TraI/MobA(P) family conjugative relaxase [Xanthomonas phaseoli]
MIAKHVPMRVVKKSDFRELVEYLNDPQAKQERVGRVTVTNCVQDNALDAALEVQATQALNTRTEADKTYH
LLISFREGENPAPEVLEAIEARVCAALGYADHQRVSAVHHDTDNLHIHVAINKIHPTRHTIHTPYNDYKT
LGEICEKLEREYGLEADNHTARKTAGENRAGDMERHAGVESLLGWIKRECADQIKSAQSWAELHAVMQRN
GLELRERGNGLVITDGAGQSVKASSIARELSKAKLEARFGAFESPVARTPSAASVQARRTQAPPVEKVGS
RPPPRSKGRTPSLAALGVLHVKSGSRYEQRPIYAKQVSTVELYARYKAEQQNLGAARNDAIARARAERDR
QIEAVKRSGRLKRAAIKLMRGPGVNKKLLYAIASKSLQEGVQQANADYLKARDAAYATHHRRAWADWLQI
KAKQGDAEALAALRARESRQSRSRNIVGGQQARRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGELLNV
SRGAGDHGVEAALRMAIYRYGERITVNGSDEFKERVAQVAAAARLNVSFEDAALDKRRQQLVDAAGAREK
LAEAAVPGKTPEFAQAQASRAGAFHEDALSERDAAASRPITPANQEQAHEQRRTRADDAAVQRGNDRGRS
DRGRDGAATGVRTGRALGRPTGAGRFGVSRGAAGADKPHVGRVGAAPPPASTHRLRNLSQLGVVQFARGS
EVLLPRHVPGRVGEQQAERDNGLRRGIHRAGGITGPGLAAADRYIAERESKRVKGFDIQKNRRYNENDAG
AVKFAGLRQVEGESLALLRRDDEVVVLAVDATTARRIKRLSVGDDVSLTSKGTLKTKGRSR
MIAKHVPMRVVKKSDFRELVEYLNDPQAKQERVGRVTVTNCVQDNALDAALEVQATQALNTRTEADKTYH
LLISFREGENPAPEVLEAIEARVCAALGYADHQRVSAVHHDTDNLHIHVAINKIHPTRHTIHTPYNDYKT
LGEICEKLEREYGLEADNHTARKTAGENRAGDMERHAGVESLLGWIKRECADQIKSAQSWAELHAVMQRN
GLELRERGNGLVITDGAGQSVKASSIARELSKAKLEARFGAFESPVARTPSAASVQARRTQAPPVEKVGS
RPPPRSKGRTPSLAALGVLHVKSGSRYEQRPIYAKQVSTVELYARYKAEQQNLGAARNDAIARARAERDR
QIEAVKRSGRLKRAAIKLMRGPGVNKKLLYAIASKSLQEGVQQANADYLKARDAAYATHHRRAWADWLQI
KAKQGDAEALAALRARESRQSRSRNIVGGQQARRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGELLNV
SRGAGDHGVEAALRMAIYRYGERITVNGSDEFKERVAQVAAAARLNVSFEDAALDKRRQQLVDAAGAREK
LAEAAVPGKTPEFAQAQASRAGAFHEDALSERDAAASRPITPANQEQAHEQRRTRADDAAVQRGNDRGRS
DRGRDGAATGVRTGRALGRPTGAGRFGVSRGAAGADKPHVGRVGAAPPPASTHRLRNLSQLGVVQFARGS
EVLLPRHVPGRVGEQQAERDNGLRRGIHRAGGITGPGLAAADRYIAERESKRVKGFDIQKNRRYNENDAG
AVKFAGLRQVEGESLALLRRDDEVVVLAVDATTARRIKRLSVGDDVSLTSKGTLKTKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 7143 | GenBank | WP_017121488 |
| Name | WP_017121488_pXAM48 |
UniProt ID | _ |
| Length | 117 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 117 a.a. Molecular weight: 12753.84 Da Isoelectric Point: 9.5971
>WP_017121488.1 MULTISPECIES: conjugal transfer transcriptional regulator TraJ [Xanthomonas]
MQDKVTRKSSPPIKVYCLPDERAAVQAKADAAGLSLSAYLLRVGMGYEIQGILDHRRVHDLALVNGDLGR
LGGLLKLWLTNDARVADFSPATIRALLAKIEATQDELRAVMTQVVRG
MQDKVTRKSSPPIKVYCLPDERAAVQAKADAAGLSLSAYLLRVGMGYEIQGILDHRRVHDLALVNGDLGR
LGGLLKLWLTNDARVADFSPATIRALLAKIEATQDELRAVMTQVVRG
Protein domains
No domain identified.
Protein structure
No available structure.
T4CP
| ID | 14859 | GenBank | WP_017121486 |
| Name | t4cp2_K9838_RS22670_pXAM48 |
UniProt ID | _ |
| Length | 645 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 645 a.a. Molecular weight: 71775.14 Da Isoelectric Point: 8.7669
>WP_017121486.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Xanthomonas]
MREKPNNAVGPQVRGSRAKKNKLVPALALTSMAAGLQAATQFFAYRFSYQPALGMNFNHAYAPWSILSWY
SKWGNLYHDYFFQAANVGAMVAAGGLIGTALVKMVGANSSKANEYLHGSARWANKKDIEQSGLLGNDEGV
YVGAWEDKDGTLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSTVVTDLKGELWAMTAGWRQKHA
KNKVIRFEPATLNGSACWNPLDEIRIATEYEVGDVQNLATLIVDPDGKGLESHWQKTSQALLVGVILHVL
YKAKNEGTPATLPYVDRIMSDPDRDVSELWMEMTQYGHVNGENHPVVGSAGRDMMDRPEEEGGSVLSTAK
SYLALYRDPVVARNVSKSEFRIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMEFERV
LADMPWWRRMLAKIGFSQVAHSYVRSKKSYKHRLLGMIDEFPSLGKLEIIQESLAFLAGYGIKFYLICQD
LNQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVVKEQITTSGKRASAILGQVSRTI
QEVQRPLLTVDECLRMPGPRKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFTARAAVPEPKFSDK
LRLVHEPAAGEAITI
MREKPNNAVGPQVRGSRAKKNKLVPALALTSMAAGLQAATQFFAYRFSYQPALGMNFNHAYAPWSILSWY
SKWGNLYHDYFFQAANVGAMVAAGGLIGTALVKMVGANSSKANEYLHGSARWANKKDIEQSGLLGNDEGV
YVGAWEDKDGTLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSTVVTDLKGELWAMTAGWRQKHA
KNKVIRFEPATLNGSACWNPLDEIRIATEYEVGDVQNLATLIVDPDGKGLESHWQKTSQALLVGVILHVL
YKAKNEGTPATLPYVDRIMSDPDRDVSELWMEMTQYGHVNGENHPVVGSAGRDMMDRPEEEGGSVLSTAK
SYLALYRDPVVARNVSKSEFRIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMEFERV
LADMPWWRRMLAKIGFSQVAHSYVRSKKSYKHRLLGMIDEFPSLGKLEIIQESLAFLAGYGIKFYLICQD
LNQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVVKEQITTSGKRASAILGQVSRTI
QEVQRPLLTVDECLRMPGPRKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFTARAAVPEPKFSDK
LRLVHEPAAGEAITI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 14860 | GenBank | WP_017121643 |
| Name | t4cp2_K9838_RS22825_pXAM48 |
UniProt ID | _ |
| Length | 848 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 848 a.a. Molecular weight: 95087.03 Da Isoelectric Point: 6.4799
>WP_017121643.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Xanthomonas]
MLQVITIAIAVLGAVLLVALFSLVLRANADLRLQKHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWF
YRGADNASATEAERELISFRINQALAPLGNGWMVHVDAVRRPAPSYSDPSLSHFPDPVSAAIDEERRRLF
ESLGTLYEGFFIITVTWFPPILAERKFVELMFHDDADKPDQKRRTAHLIQHFKREVQNLEGRLSAAVELE
RLRGVKVMQEDGSTVTHDQQLQWLQFCVTGLNHPVQLPSNPMYIDSLIGGQELYTGVVPKIGRHFIQVVA
IEGFPLESSPGILSKLAELPIEYRWASRFIFLDHHEAVSQLEKFRKKWKQKIRGFFDQVFNTNSSHVDED
AVSMVADAASAIAETNSGLVSQGYYTSVVVLMSENRHLVEASARTLEKAINALAFTARVETINTMDAYLG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
GIIFGPTRTGKSTKLGLIAFQWRRYLGARIYAFDKGLSMYPTCKAARGRHFTIASHTDKLAFAPLSRLDT
RQRRAWAMEWIDTILALNGVITTPAQRNEIAQAIMSMHKSESRTLSEFTVTVQDEEIREALKPYTVDGDM
RDLLDAEEDGLDLADFMTFEIEQLMRLDERFALPVLLYLFMQIEESLSEEDARPTLLILDEAWLMLAHPA
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNKR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIATIRKLEALHGEAWVHEWLRMKGLD
LNDYGVAS
MLQVITIAIAVLGAVLLVALFSLVLRANADLRLQKHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWF
YRGADNASATEAERELISFRINQALAPLGNGWMVHVDAVRRPAPSYSDPSLSHFPDPVSAAIDEERRRLF
ESLGTLYEGFFIITVTWFPPILAERKFVELMFHDDADKPDQKRRTAHLIQHFKREVQNLEGRLSAAVELE
RLRGVKVMQEDGSTVTHDQQLQWLQFCVTGLNHPVQLPSNPMYIDSLIGGQELYTGVVPKIGRHFIQVVA
IEGFPLESSPGILSKLAELPIEYRWASRFIFLDHHEAVSQLEKFRKKWKQKIRGFFDQVFNTNSSHVDED
AVSMVADAASAIAETNSGLVSQGYYTSVVVLMSENRHLVEASARTLEKAINALAFTARVETINTMDAYLG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
GIIFGPTRTGKSTKLGLIAFQWRRYLGARIYAFDKGLSMYPTCKAARGRHFTIASHTDKLAFAPLSRLDT
RQRRAWAMEWIDTILALNGVITTPAQRNEIAQAIMSMHKSESRTLSEFTVTVQDEEIREALKPYTVDGDM
RDLLDAEEDGLDLADFMTFEIEQLMRLDERFALPVLLYLFMQIEESLSEEDARPTLLILDEAWLMLAHPA
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNKR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIATIRKLEALHGEAWVHEWLRMKGLD
LNDYGVAS
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 34539..44963
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| K9838_RS22760 (K9838_22750) | 30677..31375 | + | 699 | WP_005918428 | YecA family protein | - |
| K9838_RS22765 (K9838_22755) | 31387..31995 | + | 609 | WP_229014504 | recombinase family protein | - |
| K9838_RS22770 (K9838_22760) | 32106..32465 | - | 360 | WP_017121476 | FxLYD domain-containing protein | - |
| K9838_RS22775 (K9838_22765) | 32477..33232 | - | 756 | WP_017121475 | TraX family protein | - |
| K9838_RS22780 (K9838_22770) | 33382..34074 | - | 693 | WP_017121474 | transglycosylase SLT domain-containing protein | - |
| K9838_RS22785 (K9838_22775) | 34077..34520 | - | 444 | WP_017121473 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| K9838_RS22790 (K9838_22780) | 34539..36146 | - | 1608 | WP_229014493 | P-type conjugative transfer protein TrbL | virB6 |
| K9838_RS22795 (K9838_22785) | 36152..36379 | - | 228 | WP_017121637 | hypothetical protein | - |
| K9838_RS22800 (K9838_22790) | 36392..37171 | - | 780 | WP_017121638 | P-type conjugative transfer protein TrbJ | virB5 |
| K9838_RS22805 (K9838_22795) | 37190..38617 | - | 1428 | WP_017121639 | TrbI/VirB10 family protein | virB10 |
| K9838_RS22810 (K9838_22800) | 38623..39123 | - | 501 | WP_229014494 | conjugal transfer protein TrbH | - |
| K9838_RS22815 (K9838_22805) | 39126..40016 | - | 891 | WP_017121641 | P-type conjugative transfer protein TrbG | virB9 |
| K9838_RS22820 (K9838_22810) | 40032..40745 | - | 714 | WP_017121642 | VirB8/TrbF family protein | virB8 |
| K9838_RS22825 (K9838_22815) | 40742..43288 | - | 2547 | WP_017121643 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| K9838_RS22830 (K9838_22820) | 43276..43596 | - | 321 | WP_017121644 | conjugal transfer protein TrbD | virB3 |
| K9838_RS22835 (K9838_22825) | 43599..43991 | - | 393 | WP_017121645 | TrbC/VirB2 family protein | virB2 |
| K9838_RS22840 (K9838_22830) | 44004..44963 | - | 960 | WP_017121646 | P-type conjugative transfer ATPase TrbB | virB11 |
| K9838_RS22845 (K9838_22835) | 45205..45567 | - | 363 | WP_017121647 | transcriptional regulator | - |
| K9838_RS22850 (K9838_22840) | 45678..46040 | + | 363 | WP_017121648 | single-stranded DNA-binding protein | - |
| K9838_RS22855 (K9838_22845) | 46139..47224 | + | 1086 | WP_086020813 | plasmid replication initiator TrfA | - |
| K9838_RS22860 (K9838_22850) | 48404..48679 | - | 276 | Protein_50 | replication protein C, IncQ-type | - |
Host bacterium
| ID | 20529 | GenBank | NZ_CP083579 |
| Plasmid name | pXAM48 | Incompatibility group | - |
| Plasmid size | 48702 bp | Coordinate of oriT [Strand] | 7080..7183 [-] |
| Host baterium | Xanthomonas phaseoli pv. manihotis strain CHN01 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |