Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 116155 |
| Name | oriT_A18/3m|p_unnamed3  |
| Organism | Phyllobacterium zundukense strain A18/3m |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP104970 (189717..189745 [-], 29 nt) |
| oriT length | 29 nt |
| IRs (inverted repeats) | 14..19, 24..29 (CGTCGC..GCGACG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 29 nt
>oriT_A18/3m|p_unnamed3
AGGGCGCAATATACGTCGCTGGCGCGACG
AGGGCGCAATATACGTCGCTGGCGCGACG
Visualization of oriT structure
Relaxase
| ID | 10332 | GenBank | WP_262290986 |
| Name | traA_N8E88_RS02670_A18/3m|p_unnamed3 |
UniProt ID | _ |
| Length | 1538 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1538 a.a. Molecular weight: 169775.44 Da Isoelectric Point: 8.7752
>WP_262290986.1 Ti-type conjugative transfer relaxase TraA [Phyllobacterium zundukense]
MAIMFIRGQVISRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGASELVHEELALPDEIPAWLRTAIDG
RSVAGASEVLWNAVDAFEKRADAQLARELIIALPEELSRAENVALVREFSENFTSKGMIADWVYHDKDGN
PHIHLMTALRPLTEEGFGPKKIAVLGENGEPLRVVTPDRPGGKIVYKLWAGDKETMKAWKIAWAETANRH
LALGGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELYFAPADLARRQEMADRLLADPELLLKQL
GNERSTFDERDIAKALHRYVDNPSDFANIRARLMASDNLVMLKPQEVDAETGRAAEPAIFTTRDILRVEY
DMAQSAQVLSERKGFAVSSRHVAAAIKSVETGDPEKPFQLDAEQVDAVRHVTGDRGIAAVVGLAGAGKST
LLAAARVAWESDGRRVIGAALAGKAAEGLEDSSGIRSRTLASLELAWAGGRGRLERGDVLVIDEAGMVSS
QQMARVLKIAEEAQAKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREQWAREASRLFARSEV
ERGLDVYALHGHLVEAQTRDEIVGRIVADWTDTRRQLLRKSVLEGNSDRLRGDELLVLAHTNDDVKRLNA
ALRHVMTGEGALGDNRAFQTERGTREFAAGDRIIFLKNARFLERRADHLGPQYVKNGMLGTVVSTSDKRG
RTLISVRLDNGRDVIFSEDSYRNVDHGYAATIHKSQGVTVDRTFVLATGMMDQHLTYVAMTRHRDRADLY
AAKEDFEARPDWGRKARVDHMAGVTGELIQEGMAKFRDADDVEASPYADIKTDGGATHRLWGVSLPKAIE
RGGVSTGDTVTLRKDGIENVTVKVPVIDAETGSKRFVERLVERNVWTAKQIETAEARESRIELESHRPEL
FGQLVGRLSRSGAKTTTLDFESEAGYRAHAQDFAWRRGIDHLSLAAAEMEEGVSRRLAWVADKREKVAKL
WERASVAPGFAIDRERRASHDEERSDTQILPEAISGGRYLIPPTTVFRRSADEDARLAQLSSPAWRERED
ILRPLLEKIYRDPDAALVHLNALASDAGIEPRKLADDVAIAPARLGRLRGSALTVGGRMACEERSVATAT
LTQLLPLIRAHATAFRRDAERFGIREQMRRSHMSLSVPALSGRAMARLGEIEAVRERGGDDTYRNAFALA
VEDRATVQEIKAVSEALTARFGWSAFTPKADIVAERNMIERMPEDLTPEKREALTTLFESVKRFAEAQHL
TERQDRSKIVAAASADPEMQNPAVLPMLAAVTAFKTPVDEEARFRALSAPHYRQQRASLAEAAVRVWRDP
AGAVSRIEELLVKGFAAERIAAAISNDPAAYSALRGSDRIMDLMLAAGWERKGALRSVPEAAARLRSLGS
SYTGALDAESQAIAEERRRMAVAIPGLSKEAEDVLARLATEVKKGDRKLGAIAGSIDPDIRREFAAVSRA
LDERFGRNAILREEKDAVNRVPPAHRPAFEAMRDRLKVLQQAVRMEASQNIISERRQRTINRARGVNL
MAIMFIRGQVISRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGASELVHEELALPDEIPAWLRTAIDG
RSVAGASEVLWNAVDAFEKRADAQLARELIIALPEELSRAENVALVREFSENFTSKGMIADWVYHDKDGN
PHIHLMTALRPLTEEGFGPKKIAVLGENGEPLRVVTPDRPGGKIVYKLWAGDKETMKAWKIAWAETANRH
LALGGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELYFAPADLARRQEMADRLLADPELLLKQL
GNERSTFDERDIAKALHRYVDNPSDFANIRARLMASDNLVMLKPQEVDAETGRAAEPAIFTTRDILRVEY
DMAQSAQVLSERKGFAVSSRHVAAAIKSVETGDPEKPFQLDAEQVDAVRHVTGDRGIAAVVGLAGAGKST
LLAAARVAWESDGRRVIGAALAGKAAEGLEDSSGIRSRTLASLELAWAGGRGRLERGDVLVIDEAGMVSS
QQMARVLKIAEEAQAKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREQWAREASRLFARSEV
ERGLDVYALHGHLVEAQTRDEIVGRIVADWTDTRRQLLRKSVLEGNSDRLRGDELLVLAHTNDDVKRLNA
ALRHVMTGEGALGDNRAFQTERGTREFAAGDRIIFLKNARFLERRADHLGPQYVKNGMLGTVVSTSDKRG
RTLISVRLDNGRDVIFSEDSYRNVDHGYAATIHKSQGVTVDRTFVLATGMMDQHLTYVAMTRHRDRADLY
AAKEDFEARPDWGRKARVDHMAGVTGELIQEGMAKFRDADDVEASPYADIKTDGGATHRLWGVSLPKAIE
RGGVSTGDTVTLRKDGIENVTVKVPVIDAETGSKRFVERLVERNVWTAKQIETAEARESRIELESHRPEL
FGQLVGRLSRSGAKTTTLDFESEAGYRAHAQDFAWRRGIDHLSLAAAEMEEGVSRRLAWVADKREKVAKL
WERASVAPGFAIDRERRASHDEERSDTQILPEAISGGRYLIPPTTVFRRSADEDARLAQLSSPAWRERED
ILRPLLEKIYRDPDAALVHLNALASDAGIEPRKLADDVAIAPARLGRLRGSALTVGGRMACEERSVATAT
LTQLLPLIRAHATAFRRDAERFGIREQMRRSHMSLSVPALSGRAMARLGEIEAVRERGGDDTYRNAFALA
VEDRATVQEIKAVSEALTARFGWSAFTPKADIVAERNMIERMPEDLTPEKREALTTLFESVKRFAEAQHL
TERQDRSKIVAAASADPEMQNPAVLPMLAAVTAFKTPVDEEARFRALSAPHYRQQRASLAEAAVRVWRDP
AGAVSRIEELLVKGFAAERIAAAISNDPAAYSALRGSDRIMDLMLAAGWERKGALRSVPEAAARLRSLGS
SYTGALDAESQAIAEERRRMAVAIPGLSKEAEDVLARLATEVKKGDRKLGAIAGSIDPDIRREFAAVSRA
LDERFGRNAILREEKDAVNRVPPAHRPAFEAMRDRLKVLQQAVRMEASQNIISERRQRTINRARGVNL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 12082 | GenBank | WP_262290989 |
| Name | traG_N8E88_RS02685_A18/3m|p_unnamed3 |
UniProt ID | _ |
| Length | 637 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 637 a.a. Molecular weight: 70053.08 Da Isoelectric Point: 9.3908
>WP_262290989.1 Ti-type conjugative transfer system protein TraG [Phyllobacterium zundukense]
MALKGKLHPSQLLVLVPIAVTVMTIYIVGWRWPGLASGLTGKAEYWFLRAGPVPALLFGPLGGLLTVWAL
PLHRRRPIAVAGLICFLAVFAFYALREYGRLALSVNQGIVTWDRALSYLDMVAALGALAGFIASAVAARI
SIVVPEAVKRAKRGTFGDADWLPMAAVGKLFPADGEIVVGERYRVDKEIVHELPFDPSDRGTWGQGGKAP
LLTFRQDFDSTHMLFFAGSGGFKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTHTLGREVMVLDPT
NPIMGFNVLDGIAASKHKEEDIVGIAHMLLSESARFESSTGSYFQNQAHNLLTGLLAHVMLSPDYAGRRH
LRSLRQIVSEPEPSVLAMLRDIQENAQSTFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVTGKKDVFLNIPASILRSYPGIGRVIIGSLINAMVQADGAFKRRALFMLDEVDLLGYMRVL
EEARDRGRKYGITMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVEG
RSRNLGWDTKNGGTRKSESVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDAAAK
ANRFVTL
MALKGKLHPSQLLVLVPIAVTVMTIYIVGWRWPGLASGLTGKAEYWFLRAGPVPALLFGPLGGLLTVWAL
PLHRRRPIAVAGLICFLAVFAFYALREYGRLALSVNQGIVTWDRALSYLDMVAALGALAGFIASAVAARI
SIVVPEAVKRAKRGTFGDADWLPMAAVGKLFPADGEIVVGERYRVDKEIVHELPFDPSDRGTWGQGGKAP
LLTFRQDFDSTHMLFFAGSGGFKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTHTLGREVMVLDPT
NPIMGFNVLDGIAASKHKEEDIVGIAHMLLSESARFESSTGSYFQNQAHNLLTGLLAHVMLSPDYAGRRH
LRSLRQIVSEPEPSVLAMLRDIQENAQSTFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVTGKKDVFLNIPASILRSYPGIGRVIIGSLINAMVQADGAFKRRALFMLDEVDLLGYMRVL
EEARDRGRKYGITMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVEG
RSRNLGWDTKNGGTRKSESVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDAAAK
ANRFVTL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 12083 | GenBank | WP_262291083 |
| Name | t4cp2_N8E88_RS03775_A18/3m|p_unnamed3 |
UniProt ID | _ |
| Length | 672 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 672 a.a. Molecular weight: 74215.45 Da Isoelectric Point: 6.0270
>WP_262291083.1 conjugal transfer protein TraG [Phyllobacterium zundukense]
MPATRVLWSQIFVVLLIVFIMVWAATQWTAWRLGFQPQLGTPWFELASLPIYPPPALLWWWYFYDAYAPH
VFIEGGAIAASGGLIAIGAAVAMSIWRAREAKDVHTYGSARWAEREEIERAGLLGDDGVVLGRYDDAYLR
HDGAEHVLCFAPTRSGKGVGLVVPTLLTWPGSAIVHDIKGENWELTAGFRARHGRVLLFDPTNPNSAAYN
PLLEVRKGEWEVRDVQNVADVLVDPEGSLEKRNHWEKTSHSLLVGAILHVLYAEKDKTLAGVAAFLSDPR
RPIESTLAAMMTTQHLGEKGPHPVIASAARELLNKSDNERSGVLSTAMSFLGLYRDPVVATVTRRCDWRI
ADIVGEDQPATLYLVVPPSDISRTKPLVRLVLNQIGRRLTEDLHARDRRHRVLMMLDEFPALGRLDFFES
ALAFMAGYGIKAFLIAQSLNQIEKAYGPNNSILDNCHVRASFATNDERTAKHVSDSLGTATEMRAMQNYA
GHRLAPWLSHLMVSRSETARPLLTPGEVMQLPPDDEIVMVAGIAPIRTKKARYYEDMRLSQRVVPAPVSG
KPGDRPLSADDWSNEAPIAVNDRTSERAHGAEAVLSDGAEGTDDTANAGLRREPGLEAHKEIVPEPASSP
INEFDLDADEPERAALSARTLTRRMGQVARQASMDPNDGVEL
MPATRVLWSQIFVVLLIVFIMVWAATQWTAWRLGFQPQLGTPWFELASLPIYPPPALLWWWYFYDAYAPH
VFIEGGAIAASGGLIAIGAAVAMSIWRAREAKDVHTYGSARWAEREEIERAGLLGDDGVVLGRYDDAYLR
HDGAEHVLCFAPTRSGKGVGLVVPTLLTWPGSAIVHDIKGENWELTAGFRARHGRVLLFDPTNPNSAAYN
PLLEVRKGEWEVRDVQNVADVLVDPEGSLEKRNHWEKTSHSLLVGAILHVLYAEKDKTLAGVAAFLSDPR
RPIESTLAAMMTTQHLGEKGPHPVIASAARELLNKSDNERSGVLSTAMSFLGLYRDPVVATVTRRCDWRI
ADIVGEDQPATLYLVVPPSDISRTKPLVRLVLNQIGRRLTEDLHARDRRHRVLMMLDEFPALGRLDFFES
ALAFMAGYGIKAFLIAQSLNQIEKAYGPNNSILDNCHVRASFATNDERTAKHVSDSLGTATEMRAMQNYA
GHRLAPWLSHLMVSRSETARPLLTPGEVMQLPPDDEIVMVAGIAPIRTKKARYYEDMRLSQRVVPAPVSG
KPGDRPLSADDWSNEAPIAVNDRTSERAHGAEAVLSDGAEGTDDTANAGLRREPGLEAHKEIVPEPASSP
INEFDLDADEPERAALSARTLTRRMGQVARQASMDPNDGVEL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 230236..239790
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| N8E88_RS02865 (N8E88_02870) | 225445..227589 | - | 2145 | WP_262291017 | ParB/RepB/Spo0J family partition protein | - |
| N8E88_RS02870 (N8E88_02875) | 227886..228803 | + | 918 | WP_262291018 | DMT family transporter | - |
| N8E88_RS02875 (N8E88_02880) | 228763..229416 | - | 654 | WP_315975197 | TetR/AcrR family transcriptional regulator | - |
| N8E88_RS02880 (N8E88_02885) | 229587..230111 | + | 525 | WP_262291019 | DinB family protein | - |
| N8E88_RS02885 (N8E88_02890) | 230236..231231 | - | 996 | WP_262291068 | P-type DNA transfer ATPase VirB11 | virB11 |
| N8E88_RS02890 (N8E88_02895) | 231240..232415 | - | 1176 | WP_262291020 | type IV secretion system protein VirB10 | virB10 |
| N8E88_RS02895 (N8E88_02900) | 232425..233276 | - | 852 | WP_262291021 | P-type conjugative transfer protein VirB9 | virB9 |
| N8E88_RS02900 (N8E88_02905) | 233273..233944 | - | 672 | WP_262291022 | virB8 family protein | virB8 |
| N8E88_RS02905 (N8E88_02910) | 233938..234231 | - | 294 | WP_262291023 | hypothetical protein | - |
| N8E88_RS02910 (N8E88_02915) | 234279..235199 | - | 921 | WP_262291024 | type IV secretion system protein | virB6 |
| N8E88_RS02915 (N8E88_02920) | 235203..235436 | - | 234 | WP_262291025 | EexN family lipoprotein | - |
| N8E88_RS02920 (N8E88_02925) | 235433..236131 | - | 699 | WP_262291026 | P-type DNA transfer protein VirB5 | virB5 |
| N8E88_RS02925 (N8E88_02930) | 236131..238497 | - | 2367 | WP_262291027 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| N8E88_RS02930 (N8E88_02935) | 238490..238828 | - | 339 | WP_262291028 | type IV secretion system protein VirB3 | virB3 |
| N8E88_RS02935 (N8E88_02940) | 238832..239131 | - | 300 | WP_262291029 | TrbC/VirB2 family protein | virB2 |
| N8E88_RS02940 (N8E88_02945) | 239128..239790 | - | 663 | WP_262291030 | transglycosylase SLT domain-containing protein | virB1 |
| N8E88_RS02945 (N8E88_02950) | 239793..240332 | - | 540 | WP_262291031 | hypothetical protein | - |
| N8E88_RS02950 (N8E88_02955) | 240429..240782 | + | 354 | WP_262291032 | MarR family transcriptional regulator | - |
| N8E88_RS02955 (N8E88_02960) | 241098..241295 | + | 198 | WP_262291033 | hypothetical protein | - |
| N8E88_RS02960 (N8E88_02965) | 241391..241539 | - | 149 | Protein_228 | cold-shock protein | - |
| N8E88_RS02965 (N8E88_02970) | 241628..242029 | - | 402 | WP_262291034 | hypothetical protein | - |
| N8E88_RS02970 (N8E88_02975) | 242164..243379 | - | 1216 | Protein_230 | plasmid replication protein RepC | - |
| N8E88_RS02975 (N8E88_02980) | 243534..244523 | - | 990 | WP_262291035 | plasmid partitioning protein RepB | - |
Host bacterium
| ID | 16588 | GenBank | NZ_CP104970 |
| Plasmid name | A18/3m|p_unnamed3 | Incompatibility group | - |
| Plasmid size | 568546 bp | Coordinate of oriT [Strand] | 189717..189745 [-] |
| Host baterium | Phyllobacterium zundukense strain A18/3m |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | LinG, dxnH, linJ |
| Symbiosis gene | - |
| Anti-CRISPR | - |