Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 121173 |
| Name | oriT_CoDiRO|unnamed  |
| Organism | Xylella fastidiosa strain CoDiRO |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CM003178 (5981..6086 [-], 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_CoDiRO|unnamed
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTGCCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTGCCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 13367 | GenBank | WP_046417493 |
| Name | traI_RA12_RS00055_CoDiRO|unnamed |
UniProt ID | _ |
| Length | 830 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 830 a.a. Molecular weight: 92904.89 Da Isoelectric Point: 10.5707
>WP_046417493.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVKKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVMDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESHVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKRYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQAQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKEKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTNRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVRKANTDYLKARDAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQVRRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFEDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQAQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSYELMAVDKYIAERELKRVRMFDIMKHRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTNKGTLKTKGRNR
MIAKHVPMRVVKKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVMDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESHVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKRYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQAQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKEKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTNRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVRKANTDYLKARDAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQVRRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFEDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQAQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSYELMAVDKYIAERELKRVRMFDIMKHRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTNKGTLKTKGRNR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 15665 | GenBank | WP_046417494 |
| Name | t4cp2_RA12_RS00060_CoDiRO|unnamed |
UniProt ID | _ |
| Length | 644 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 644 a.a. Molecular weight: 72074.59 Da Isoelectric Point: 8.5743
>WP_046417494.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNHNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGTNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDKL
RFVHEPTLLDEIKI
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNHNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGTNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDKL
RFVHEPTLLDEIKI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 15666 | GenBank | WP_046417530 |
| Name | t4cp2_RA12_RS00155_CoDiRO|unnamed |
UniProt ID | _ |
| Length | 854 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 854 a.a. Molecular weight: 95693.78 Da Isoelectric Point: 6.3113
>WP_046417530.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALLGAVLLIWLFLLVQRANADLRLKNHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASLDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESMGTLYEGVFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHIDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEHSARQLEKAINALAFTARVETINTMDAYVG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSESKSSTLSEFIVTVQDAVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLAHTT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLRLKGLR
LDEYVSPNDYGVAA
MFQIITIAIALLGAVLLIWLFLLVQRANADLRLKNHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASLDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESMGTLYEGVFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHIDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEHSARQLEKAINALAFTARVETINTMDAYVG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSESKSSTLSEFIVTVQDAVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLAHTT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLRLKGLR
LDEYVSPNDYGVAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 22487..32765
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RA12_RS00085 (RA12_11240) | 18217..18774 | - | 558 | WP_046417502 | recombinase family protein | - |
| RA12_RS00090 (RA12_11245) | 18862..19149 | - | 288 | WP_004085905 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| RA12_RS00095 (RA12_11250) | 19142..19384 | - | 243 | WP_004085758 | type II toxin-antitoxin system ParD family antitoxin | - |
| RA12_RS13280 | 19579..19665 | + | 87 | Protein_19 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| RA12_RS00100 (RA12_11255) | 19802..20122 | + | 321 | WP_046417511 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| RA12_RS00105 (RA12_11260) | 20252..20578 | + | 327 | WP_004091396 | DNA-binding protein | - |
| RA12_RS12840 | 20953..21126 | - | 174 | WP_155641416 | hypothetical protein | - |
| RA12_RS00110 (RA12_11265) | 21128..21382 | - | 255 | WP_230950296 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| RA12_RS00115 (RA12_11270) | 21372..21851 | + | 480 | Protein_24 | Tn3 family transposase | - |
| RA12_RS11510 | 21747..22481 | - | 735 | WP_232755968 | conjugal transfer protein TrbN | - |
| RA12_RS00120 (RA12_11275) | 22487..23884 | - | 1398 | WP_046417516 | P-type conjugative transfer protein TrbL | virB6 |
| RA12_RS12845 (RA12_11280) | 23890..24204 | - | 315 | WP_155561293 | EexN family lipoprotein | - |
| RA12_RS00130 (RA12_11285) | 24217..25002 | - | 786 | WP_046417519 | P-type conjugative transfer protein TrbJ | virB5 |
| RA12_RS00135 (RA12_11290) | 25021..26421 | - | 1401 | WP_046417521 | TrbI/VirB10 family protein | virB10 |
| RA12_RS00140 (RA12_11295) | 26427..26903 | - | 477 | WP_046417523 | conjugal transfer protein TrbH | - |
| RA12_RS00145 (RA12_11300) | 26906..27796 | - | 891 | WP_046417527 | P-type conjugative transfer protein TrbG | virB9 |
| RA12_RS00150 (RA12_11305) | 27813..28529 | - | 717 | WP_046417528 | conjugal transfer protein TrbF | virB8 |
| RA12_RS00155 (RA12_11310) | 28526..31090 | - | 2565 | WP_046417530 | conjugal transfer protein TrbE | virb4 |
| RA12_RS00160 (RA12_11315) | 31078..31398 | - | 321 | WP_046417532 | conjugal transfer protein TrbD | virB3 |
| RA12_RS00165 (RA12_11320) | 31401..31793 | - | 393 | WP_046417535 | TrbC/VirB2 family protein | virB2 |
| RA12_RS00170 (RA12_11325) | 31806..32765 | - | 960 | WP_046417547 | P-type conjugative transfer ATPase TrbB | virB11 |
| RA12_RS00175 (RA12_11330) | 32963..33319 | - | 357 | WP_012382841 | transcriptional regulator | - |
| RA12_RS00180 (RA12_11335) | 33437..33796 | + | 360 | WP_004091494 | single-stranded DNA-binding protein | - |
| RA12_RS00185 (RA12_11340) | 33840..34187 | + | 348 | WP_050812600 | hypothetical protein | - |
| RA12_RS00190 (RA12_11345) | 34231..35142 | + | 912 | WP_004091489 | replication protein RepA | - |
Host bacterium
| ID | 21601 | GenBank | NZ_CM003178 |
| Plasmid name | CoDiRO|unnamed | Incompatibility group | - |
| Plasmid size | 35318 bp | Coordinate of oriT [Strand] | 5981..6086 [-] |
| Host baterium | Xylella fastidiosa strain CoDiRO |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |