Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113989 |
| Name | oriT_pCf164_LMB-1  |
| Organism | Citrobacter freundii strain 164 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_MH475146 (68686..68836 [-], 151 nt) |
| oriT length | 151 nt |
| IRs (inverted repeats) | 93..98, 106..111 (TGGCCT..AGGCCA) 12..17, 24..29 (AACCCT..AGGGTT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 151 nt
>oriT_pCf164_LMB-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8984 | GenBank | WP_088212660 |
| Name | mobH_HTT67_RS00385_pCf164_LMB-1 |
UniProt ID | _ |
| Length | 990 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 990 a.a. Molecular weight: 109452.09 Da Isoelectric Point: 4.9964
>WP_088212660.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPRLDANKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQPKEKKVDVTSPVEEPQRK
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPRLDANKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQPKEKKVDVTSPVEEPQRK
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 10418 | GenBank | WP_088212670 |
| Name | traC_HTT67_RS00300_pCf164_LMB-1 |
UniProt ID | _ |
| Length | 815 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 815 a.a. Molecular weight: 92632.91 Da Isoelectric Point: 5.9216
>WP_088212670.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYVGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYVGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 10419 | GenBank | WP_000178857 |
| Name | traD_HTT67_RS00380_pCf164_LMB-1 |
UniProt ID | _ |
| Length | 621 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 621 a.a. Molecular weight: 69225.71 Da Isoelectric Point: 6.9403
>WP_000178857.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 45606..70752
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTT67_RS00240 | 40733..41641 | - | 909 | WP_088212677 | hypothetical protein | - |
| HTT67_RS00245 | 41652..42620 | - | 969 | WP_088212676 | AAA family ATPase | - |
| HTT67_RS00250 | 42840..43025 | - | 186 | WP_001186917 | hypothetical protein | - |
| HTT67_RS00255 | 43329..43649 | - | 321 | WP_000547566 | hypothetical protein | - |
| HTT67_RS00260 | 43943..44584 | + | 642 | WP_088212675 | hypothetical protein | - |
| HTT67_RS00265 | 44707..45567 | + | 861 | WP_088212674 | hypothetical protein | - |
| HTT67_RS00270 | 45606..48416 | - | 2811 | WP_088212673 | conjugal transfer mating pair stabilization protein TraN | traN |
| HTT67_RS00275 | 48520..49524 | - | 1005 | WP_005507569 | TraU family protein | traU |
| HTT67_RS00280 | 49524..50195 | - | 672 | WP_088212672 | EAL domain-containing protein | - |
| HTT67_RS00285 | 50192..51457 | - | 1266 | WP_088212671 | TrbC family F-type conjugative pilus assembly protein | traW |
| HTT67_RS00290 | 51420..51950 | - | 531 | WP_001010738 | S26 family signal peptidase | - |
| HTT67_RS00295 | 51947..52264 | - | 318 | WP_000351984 | hypothetical protein | - |
| HTT67_RS00300 | 52279..54726 | - | 2448 | WP_088212670 | type IV secretion system protein TraC | virb4 |
| HTT67_RS00305 | 54723..55430 | - | 708 | WP_001259346 | DsbC family protein | - |
| HTT67_RS00310 | 55579..61065 | - | 5487 | WP_088212669 | Ig-like domain-containing protein | - |
| HTT67_RS00315 | 61266..61658 | - | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| HTT67_RS00320 | 61662..62240 | - | 579 | WP_088212668 | type IV conjugative transfer system lipoprotein TraV | traV |
| HTT67_RS00325 | 62237..63550 | - | 1314 | WP_172693100 | TraB/VirB10 family protein | traB |
| HTT67_RS00330 | 63550..64467 | - | 918 | WP_088212666 | type-F conjugative transfer system secretin TraK | traK |
| HTT67_RS00335 | 64451..65077 | - | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| HTT67_RS00340 | 65074..65355 | - | 282 | WP_088212665 | type IV conjugative transfer system protein TraL | traL |
| HTT67_RS00345 | 65500..65865 | - | 366 | WP_001052531 | hypothetical protein | - |
| HTT67_RS00350 | 65877..66020 | - | 144 | WP_172693090 | hypothetical protein | - |
| HTT67_RS00355 | 66201..66863 | - | 663 | WP_088212664 | hypothetical protein | - |
| HTT67_RS00360 | 66863..67240 | - | 378 | WP_088212663 | hypothetical protein | - |
| HTT67_RS00365 | 67250..67696 | - | 447 | WP_000122507 | hypothetical protein | - |
| HTT67_RS00370 | 67706..68335 | - | 630 | WP_088212662 | DUF4400 domain-containing protein | tfc7 |
| HTT67_RS00375 | 68292..68876 | - | 585 | WP_088212661 | hypothetical protein | - |
| HTT67_RS00380 | 68887..70752 | - | 1866 | WP_000178857 | conjugative transfer system coupling protein TraD | virb4 |
| HTT67_RS00385 | 70749..73721 | - | 2973 | WP_088212660 | MobH family relaxase | - |
| HTT67_RS00390 | 73889..74506 | + | 618 | WP_001249395 | hypothetical protein | - |
| HTT67_RS00395 | 74488..74721 | + | 234 | WP_001191890 | hypothetical protein | - |
Host bacterium
| ID | 14424 | GenBank | NZ_MH475146 |
| Plasmid name | pCf164_LMB-1 | Incompatibility group | IncA/C2 |
| Plasmid size | 175712 bp | Coordinate of oriT [Strand] | 68686..68836 [-] |
| Host baterium | Citrobacter freundii strain 164 |
Cargo genes
| Drug resistance gene | blaPER-2, sul1, qacE, blaLMB-1, aadA16, dfrA27, ARR-3 |
| Virulence gene | - |
| Metal resistance gene | merR, merT, merP, merC, merA, merD, merE |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |