Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107510 |
| Name | oriT_pNDM_9580  |
| Organism | Serratia marcescens strain 9580 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_MF042357 (89321..89423 [-], 103 nt) |
| oriT length | 103 nt |
| IRs (inverted repeats) | 89..94, 96..101 (AAATAA..TTATTT) 28..33, 40..45 (GCAAAA..TTTTGC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 103 nt
>oriT_pNDM_9580
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 5033 | GenBank | WP_016479978 |
| Name | traI_HTN66_RS00350_pNDM_9580 |
UniProt ID | A0A0G3B767 |
| Length | 1746 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1746 a.a. Molecular weight: 189285.41 Da Isoelectric Point: 6.0099
>WP_016479978.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWAAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQPHVALPAFDRNGRKAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADGLPDATGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWAAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQPHVALPAFDRNGRKAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADGLPDATGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 5244 | GenBank | WP_008324134 |
| Name | traC_HTN66_RS00430_pNDM_9580 |
UniProt ID | _ |
| Length | 876 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 876 a.a. Molecular weight: 98841.51 Da Isoelectric Point: 5.7676
>WP_008324134.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacterales]
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVLQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIS
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVLQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIS
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 68396..89971
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTN66_RS00355 | 64759..67066 | - | 2308 | Protein_71 | type IV conjugative transfer system coupling protein TraD | - |
| HTN66_RS00630 | 67200..67529 | - | 330 | WP_223856629 | hypothetical protein | - |
| HTN66_RS00635 | 67537..67869 | - | 333 | WP_238785714 | tetratricopeptide repeat protein | - |
| HTN66_RS00365 | 67944..68375 | - | 432 | WP_008324118 | entry exclusion protein | - |
| HTN66_RS00370 | 68396..71218 | - | 2823 | WP_008324119 | conjugal transfer mating-pair stabilization protein TraG | traG |
| HTN66_RS00375 | 71218..72564 | - | 1347 | WP_096148933 | conjugal transfer pilus assembly protein TraH | traH |
| HTN66_RS00640 | 72506..72826 | - | 321 | WP_238785715 | hypothetical protein | - |
| HTN66_RS00385 | 72991..73545 | - | 555 | WP_008324125 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| HTN66_RS00390 | 73535..73732 | - | 198 | WP_057095198 | type-F conjugative transfer system pilin chaperone TraQ | - |
| HTN66_RS00395 | 73802..74543 | - | 742 | Protein_80 | type-F conjugative transfer system pilin assembly protein TraF | - |
| HTN66_RS00400 | 74574..74762 | - | 189 | WP_008324128 | conjugal transfer protein TrbE | - |
| HTN66_RS00405 | 74794..76645 | - | 1852 | Protein_82 | type-F conjugative transfer system mating-pair stabilization protein TraN | - |
| HTN66_RS00410 | 76642..77271 | - | 630 | WP_008324130 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| HTN66_RS00415 | 77288..78274 | - | 987 | WP_042934586 | conjugal transfer pilus assembly protein TraU | traU |
| HTN66_RS00420 | 78277..78924 | - | 648 | WP_008324132 | type-F conjugative transfer system protein TraW | traW |
| HTN66_RS00425 | 78924..79271 | - | 348 | WP_008324133 | type-F conjugative transfer system protein TrbI | - |
| HTN66_RS00430 | 79268..81898 | - | 2631 | WP_008324134 | type IV secretion system protein TraC | virb4 |
| HTN66_RS00435 | 81891..82457 | - | 567 | WP_008324135 | conjugal transfer pilus-stabilizing protein TraP | - |
| HTN66_RS00440 | 82447..82848 | - | 402 | WP_016479985 | hypothetical protein | - |
| HTN66_RS00445 | 82832..83017 | - | 186 | WP_008324139 | hypothetical protein | - |
| HTN66_RS00450 | 83021..83245 | - | 225 | WP_008324141 | TraR/DksA C4-type zinc finger protein | - |
| HTN66_RS00455 | 83365..83904 | - | 540 | WP_016247533 | type IV conjugative transfer system lipoprotein TraV | traV |
| HTN66_RS00460 | 83926..85320 | - | 1395 | WP_016479986 | F-type conjugal transfer pilus assembly protein TraB | traB |
| HTN66_RS00465 | 85307..86050 | - | 744 | WP_008324157 | type-F conjugative transfer system secretin TraK | traK |
| HTN66_RS00470 | 86037..86603 | - | 567 | WP_016247535 | type IV conjugative transfer system protein TraE | traE |
| HTN66_RS00475 | 86618..86923 | - | 306 | WP_008324160 | type IV conjugative transfer system protein TraL | traL |
| HTN66_RS00480 | 87074..87424 | - | 351 | WP_016247536 | type IV conjugative transfer system pilin TraA | - |
| HTN66_RS00485 | 87482..87706 | - | 225 | WP_008324165 | TraY domain-containing protein | - |
| HTN66_RS00490 | 87793..88482 | - | 690 | WP_008324166 | hypothetical protein | - |
| HTN66_RS00495 | 88671..89063 | - | 393 | WP_008324167 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| HTN66_RS00500 | 89495..89971 | + | 477 | WP_008324168 | transglycosylase SLT domain-containing protein | - |
| HTN66_RS00505 | 90018..90548 | - | 531 | WP_008324170 | antirestriction protein | - |
| HTN66_RS00510 | 91175..92005 | - | 831 | WP_008324171 | N-6 DNA methylase | - |
| HTN66_RS00515 | 92048..92311 | - | 264 | WP_008324174 | hypothetical protein | - |
| HTN66_RS00520 | 92397..92741 | - | 345 | WP_008324177 | hypothetical protein | - |
| HTN66_RS00525 | 92788..93075 | - | 288 | WP_008324178 | hypothetical protein | - |
| HTN66_RS00530 | 93129..93503 | - | 375 | WP_008324180 | hypothetical protein | - |
| HTN66_RS00535 | 94130..94489 | - | 360 | WP_015493069 | hypothetical protein | - |
| HTN66_RS00540 | 94551..94874 | - | 324 | WP_008324183 | hypothetical protein | - |
Host bacterium
| ID | 7945 | GenBank | NZ_MF042357 |
| Plasmid name | pNDM_9580 | Incompatibility group | IncFIB |
| Plasmid size | 105614 bp | Coordinate of oriT [Strand] | 89321..89423 [-] |
| Host baterium | Serratia marcescens strain 9580 |
Cargo genes
| Drug resistance gene | blaNDM-1, rmtC, sul1 |
| Virulence gene | htpB |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |