Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114823 |
| Name | oriT_pXFAS_XYL461  |
| Organism | Xylella fastidiosa subsp. fastidiosa strain XYL461 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP109896 (38165..38270 [-], 106 nt) |
| oriT length | 106 nt |
| IRs (inverted repeats) | 68..74, 77..83 (CACCGGA..TCCGGTG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 106 nt
>oriT_pXFAS_XYL461
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTACCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTACCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 11070 | GenBank | WP_004086666 |
| Name | t4cp2_OK116_RS00015_pXFAS_XYL461 |
UniProt ID | _ |
| Length | 644 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 644 a.a. Molecular weight: 72064.60 Da Isoelectric Point: 8.5739
>WP_004086666.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNRNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKGRLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGFNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDTL
RLVHEPTLLDEIKI
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNRNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKGRLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGFNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDTL
RLVHEPTLLDEIKI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 11071 | GenBank | WP_004086690 |
| Name | t4cp2_OK116_RS00115_pXFAS_XYL461 |
UniProt ID | _ |
| Length | 854 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 854 a.a. Molecular weight: 95956.03 Da Isoelectric Point: 6.3394
>WP_004086690.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALLGTVLLIWLFLLVQRANADLRLKNHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASFDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESIDTLYEGFFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHVDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEQSARRLEKAINALAFTARVETINTMDAYLG
SLPGHGVENVRRPLLNTMNFADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSKSKASTLSEFIVTVQDEVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLSHTT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLRLKGLR
LDEYVSPNDYGVAA
MFQIITIAIALLGTVLLIWLFLLVQRANADLRLKNHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASFDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESIDTLYEGFFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHVDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEQSARRLEKAINALAFTARVETINTMDAYLG
SLPGHGVENVRRPLLNTMNFADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSKSKASTLSEFIVTVQDEVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLSHTT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLRLKGLR
LDEYVSPNDYGVAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 17977..28158
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| OK116_RS00045 (OK116_00045) | 12985..13578 | - | 594 | WP_004086728 | LPD29 domain-containing protein | - |
| OK116_RS00050 (OK116_00050) | 13755..14069 | - | 315 | WP_012382835 | TrfB-related DNA-binding protein | - |
| OK116_RS00055 (OK116_00055) | 14137..14730 | - | 594 | WP_004086726 | LPD29 domain-containing protein | - |
| OK116_RS00060 (OK116_00060) | 15061..15624 | - | 564 | WP_004086710 | recombinase family protein | - |
| OK116_RS00065 (OK116_00065) | 16167..16535 | + | 369 | WP_004086708 | hypothetical protein | - |
| OK116_RS00070 (OK116_00070) | 16532..16759 | + | 228 | WP_004086706 | hypothetical protein | - |
| OK116_RS00075 (OK116_00075) | 17372..17971 | - | 600 | WP_004086719 | conjugal transfer protein TrbN | - |
| OK116_RS00080 (OK116_00080) | 17977..19347 | - | 1371 | WP_004086703 | P-type conjugative transfer protein TrbL | virB6 |
| OK116_RS00085 (OK116_00085) | 19369..19605 | - | 237 | WP_012382834 | EexN family lipoprotein | - |
| OK116_RS00090 (OK116_00090) | 19622..20395 | - | 774 | WP_004086702 | P-type conjugative transfer protein TrbJ | virB5 |
| OK116_RS00095 (OK116_00095) | 20414..21814 | - | 1401 | WP_012382833 | TrbI/VirB10 family protein | virB10 |
| OK116_RS00100 (OK116_00100) | 21820..22296 | - | 477 | WP_004086697 | conjugal transfer protein TrbH | - |
| OK116_RS00105 (OK116_00105) | 22299..23189 | - | 891 | WP_004086695 | P-type conjugative transfer protein TrbG | virB9 |
| OK116_RS00110 (OK116_00110) | 23206..23922 | - | 717 | WP_004086692 | conjugal transfer protein TrbF | virB8 |
| OK116_RS00115 (OK116_00115) | 23919..26483 | - | 2565 | WP_004086690 | conjugal transfer protein TrbE | virb4 |
| OK116_RS00120 (OK116_00120) | 26471..26791 | - | 321 | WP_004086725 | conjugal transfer protein TrbD | virB3 |
| OK116_RS00125 (OK116_00125) | 26794..27186 | - | 393 | WP_004086717 | TrbC/VirB2 family protein | virB2 |
| OK116_RS00130 (OK116_00130) | 27199..28158 | - | 960 | WP_038231439 | P-type conjugative transfer ATPase TrbB | virB11 |
| OK116_RS00135 (OK116_00135) | 28365..28721 | - | 357 | WP_012382841 | transcriptional regulator | - |
| OK116_RS00140 (OK116_00140) | 28839..29198 | + | 360 | WP_012382840 | single-stranded DNA-binding protein | - |
| OK116_RS00145 (OK116_00145) | 29242..29598 | + | 357 | WP_004086687 | hypothetical protein | - |
| OK116_RS00150 (OK116_00150) | 29620..30531 | + | 912 | WP_004086685 | replication protein RepA | - |
| OK116_RS00155 (OK116_00155) | 31254..31574 | + | 321 | WP_012382839 | KleE stable inheritance protein | - |
| OK116_RS00160 (OK116_00160) | 31615..32811 | - | 1197 | WP_004086683 | RNA-guided endonuclease TnpB family protein | - |
| OK116_RS00165 (OK116_00165) | 32805..33059 | - | 255 | Protein_32 | recombinase family protein | - |
Host bacterium
| ID | 15258 | GenBank | NZ_CP109896 |
| Plasmid name | pXFAS_XYL461 | Incompatibility group | - |
| Plasmid size | 38297 bp | Coordinate of oriT [Strand] | 38165..38270 [-] |
| Host baterium | Xylella fastidiosa subsp. fastidiosa strain XYL461 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |