Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 111100 |
| Name | oriT_pAMA003584_NDM-1  |
| Organism | Salmonella enterica subsp. enterica serovar Kottbus strain AMA003584 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_MZ004973 (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_pAMA003584_NDM-1
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 7285 | GenBank | WP_014014966 |
| Name | mobF_KV199_RS00100_pAMA003584_NDM-1 |
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 | 8299 | GenBank | WP_014014965 |
| Name | t4cp2_KV199_RS00095_pAMA003584_NDM-1 |
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: 29105..39387
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| KV199_RS00150 | 24458..25270 | - | 813 | WP_004201164 | subclass B1 metallo-beta-lactamase NDM-1 | - |
| KV199_RS00155 | 25371..25625 | - | 255 | WP_065800077 | hypothetical protein | - |
| KV199_RS00160 | 25566..26597 | + | 1032 | WP_001395480 | IS630-like element ISEc33 family transposase | - |
| KV199_RS00165 | 26616..27362 | - | 747 | Protein_33 | IS30-like element ISAba125 family transposase | - |
| KV199_RS00170 | 27546..27950 | - | 405 | WP_129484004 | hypothetical protein | - |
| KV199_RS00175 | 28581..29093 | - | 513 | WP_029697418 | phospholipase D family protein | - |
| KV199_RS00180 | 29105..30106 | - | 1002 | WP_001076634 | ATPase, T2SS/T4P/T4SS family | virB11 |
| KV199_RS00185 | 30157..31296 | - | 1140 | WP_014014945 | type IV secretion system protein VirB10 | virB10 |
| KV199_RS00190 | 31296..32183 | - | 888 | WP_014014946 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| KV199_RS00195 | 32194..32889 | - | 696 | WP_014014947 | type IV secretion system protein | virB8 |
| KV199_RS00200 | 33108..34145 | - | 1038 | WP_014014948 | type IV secretion system protein | virB6 |
| KV199_RS00205 | 34162..34404 | - | 243 | WP_000858958 | EexN family lipoprotein | - |
| KV199_RS00210 | 34414..35115 | - | 702 | WP_014014949 | type IV secretion system protein | virB5 |
| KV199_RS00215 | 35131..37704 | - | 2574 | WP_014014950 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| KV199_RS00220 | 37705..38022 | - | 318 | WP_000462629 | VirB3 family type IV secretion system protein | virB3 |
| KV199_RS00225 | 38062..38403 | - | 342 | WP_001121032 | TrbC/VirB2 family protein | virB2 |
| KV199_RS00230 | 38605..39387 | - | 783 | WP_014014952 | lytic transglycosylase domain-containing protein | virB1 |
| KV199_RS00235 | 39451..39804 | + | 354 | WP_225988093 | H-NS family nucleoid-associated regulatory protein | - |
| KV199_RS00240 | 39808..40158 | + | 351 | WP_014014953 | hypothetical protein | - |
| KV199_RS00285 | 40137..40493 | + | 357 | WP_014014954 | hypothetical protein | - |
| KV199_RS00250 | 40497..40805 | + | 309 | WP_000733764 | hypothetical protein | - |
| KV199_RS00255 | 41090..41275 | + | 186 | WP_014014955 | ribbon-helix-helix domain-containing protein | - |
| KV199_RS00260 | 41272..41880 | - | 609 | WP_000275218 | recombinase family protein | - |
| KV199_RS00265 | 42046..42378 | - | 333 | WP_015060077 | hypothetical protein | - |
Host bacterium
| ID | 11535 | GenBank | NZ_MZ004973 |
| Plasmid name | pAMA003584_NDM-1 | Incompatibility group | IncN2 |
| Plasmid size | 42517 bp | Coordinate of oriT [Strand] | 11481..11563 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Kottbus strain AMA003584 |
Cargo genes
| Drug resistance gene | blaNDM-1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |