Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107432 |
| Name | oriT_pYNKP001-NDM  |
| Organism | Raoultella ornithinolytica strain YNKP001 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_KP900017 (11481..11563 [-], 83 nt) |
| oriT length | 83 nt |
| IRs (inverted repeats) | 27..34, 37..44 (AGTGCGAT..ATCGCACT) 13..18, 32..37 (TAAATC..GATTTA) |
| Location of nic site | 55..56 |
| Conserved sequence flanking the nic site |
GGTGTATAGC |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 83 nt
>oriT_pYNKP001-NDM
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4970 | GenBank | WP_014014966 |
| Name | mobF_HTE45_RS00100_pYNKP001-NDM |
UniProt ID | I7CZU5 |
| Length | 1068 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1068 a.a. Molecular weight: 118452.14 Da Isoelectric Point: 6.4309
>WP_014014966.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPDTSGT
ENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARDVELP
QHEHENHQHDHDKEGYGL
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPDTSGT
ENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARDVELP
QHEHENHQHDHDKEGYGL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | I7CZU5 |
T4CP
| ID | 5169 | GenBank | WP_014014965 |
| Name | t4cp2_HTE45_RS00095_pYNKP001-NDM |
UniProt ID | _ |
| Length | 510 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 510 a.a. Molecular weight: 58174.11 Da Isoelectric Point: 9.7081
>WP_014014965.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAERTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGGILQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAERTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGGILQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 27778..38060
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTE45_RS00140 (pYNKP001-NDM_0032) | 23131..23943 | - | 813 | WP_004201164 | subclass B1 metallo-beta-lactamase NDM-1 | - |
| HTE45_RS00145 | 24044..24298 | - | 255 | WP_065800077 | hypothetical protein | - |
| HTE45_RS00150 (pYNKP001-NDM_0034) | 24239..25270 | + | 1032 | WP_001395480 | IS630-like element ISEc33 family transposase | - |
| HTE45_RS00155 (pYNKP001-NDM_0035) | 25289..26035 | - | 747 | Protein_31 | IS30-like element ISAba125 family transposase | - |
| HTE45_RS00160 | 26219..26623 | - | 405 | WP_129484004 | hypothetical protein | - |
| HTE45_RS00165 (pYNKP001-NDM_0038) | 27254..27766 | - | 513 | WP_029697418 | phospholipase D family protein | - |
| HTE45_RS00170 (pYNKP001-NDM_0039) | 27778..28779 | - | 1002 | WP_001076634 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HTE45_RS00175 (pYNKP001-NDM_0040) | 28830..29969 | - | 1140 | WP_014014945 | type IV secretion system protein VirB10 | virB10 |
| HTE45_RS00180 (pYNKP001-NDM_0041) | 29969..30856 | - | 888 | WP_014014946 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HTE45_RS00185 (pYNKP001-NDM_0042) | 30867..31562 | - | 696 | WP_014014947 | type IV secretion system protein | virB8 |
| HTE45_RS00290 | 31573..31704 | - | 132 | WP_072000589 | conjugal transfer protein TraN | - |
| HTE45_RS00190 (pYNKP001-NDM_0043) | 31781..32818 | - | 1038 | WP_014014948 | type IV secretion system protein | virB6 |
| HTE45_RS00195 (pYNKP001-NDM_0044) | 32835..33077 | - | 243 | WP_000858958 | EexN family lipoprotein | - |
| HTE45_RS00200 (pYNKP001-NDM_0045) | 33087..33788 | - | 702 | WP_014014949 | type IV secretion system protein | virB5 |
| HTE45_RS00205 (pYNKP001-NDM_0046) | 33804..36377 | - | 2574 | WP_014014950 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HTE45_RS00210 (pYNKP001-NDM_0047) | 36378..36695 | - | 318 | WP_000462629 | VirB3 family type IV secretion system protein | virB3 |
| HTE45_RS00215 (pYNKP001-NDM_0048) | 36735..37076 | - | 342 | WP_001121032 | TrbC/VirB2 family protein | virB2 |
| HTE45_RS00220 (pYNKP001-NDM_0049) | 37278..38060 | - | 783 | WP_014014952 | lytic transglycosylase domain-containing protein | virB1 |
| HTE45_RS00225 (pYNKP001-NDM_0050) | 38124..38477 | + | 354 | WP_225988093 | H-NS family nucleoid-associated regulatory protein | - |
| HTE45_RS00230 (pYNKP001-NDM_0051) | 38481..38831 | + | 351 | WP_014014953 | hypothetical protein | - |
| HTE45_RS00275 (pYNKP001-NDM_0052) | 38810..39166 | + | 357 | WP_014014954 | hypothetical protein | - |
| HTE45_RS00240 (pYNKP001-NDM_0053) | 39170..39478 | + | 309 | WP_000733764 | hypothetical protein | - |
| HTE45_RS00245 (pYNKP001-NDM_0054) | 39763..39948 | + | 186 | WP_014014955 | ribbon-helix-helix domain-containing protein | - |
| HTE45_RS00250 (pYNKP001-NDM_0055) | 39945..40553 | - | 609 | WP_000275218 | recombinase family protein | - |
| HTE45_RS00255 (pYNKP001-NDM_0056) | 40719..41051 | - | 333 | WP_015060077 | hypothetical protein | - |
Host bacterium
| ID | 7867 | GenBank | NZ_KP900017 |
| Plasmid name | pYNKP001-NDM | Incompatibility group | IncN2 |
| Plasmid size | 41190 bp | Coordinate of oriT [Strand] | 11481..11563 [-] |
| Host baterium | Raoultella ornithinolytica strain YNKP001 |
Cargo genes
| Drug resistance gene | blaNDM-1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |