Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 106113 |
| Name | oriT_pNDM13-SR33  |
| Organism | Salmonella enterica subsp. enterica strain SR33 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP092912 (33954..34042 [-], 89 nt) |
| oriT length | 89 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 89 nt
>oriT_pNDM13-SR33
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4098 | GenBank | WP_071447698 |
| Name | nikB_MLD58_RS24275_pNDM13-SR33 |
UniProt ID | A0A1S7B047 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103868.35 Da Isoelectric Point: 7.4198
>WP_071447698.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMEGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMEGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A1S7B047 |
Auxiliary protein
| ID | 1805 | GenBank | WP_001283947 |
| Name | WP_001283947_pNDM13-SR33 |
UniProt ID | A0A142CMC2 |
| Length | 110 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12613.57 Da Isoelectric Point: 10.7463
>WP_001283947.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A142CMC2 |
T4CP
| ID | 4111 | GenBank | WP_001289275 |
| Name | trbC_MLD58_RS24280_pNDM13-SR33 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86957.15 Da Isoelectric Point: 6.7713
>WP_001289275.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 39420..78835
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| MLD58_RS24280 | 37136..39427 | - | 2292 | WP_001289275 | F-type conjugative transfer protein TrbC | - |
| MLD58_RS24285 | 39420..40490 | - | 1071 | WP_241420308 | IncI1-type conjugal transfer protein TrbB | trbB |
| MLD58_RS24290 | 40509..41717 | - | 1209 | WP_001383960 | IncI1-type conjugal transfer protein TrbA | trbA |
| MLD58_RS24295 | 41935..42921 | - | 987 | WP_001257838 | hypothetical protein | - |
| MLD58_RS24300 | 43194..43346 | + | 153 | WP_193793440 | Hok/Gef family protein | - |
| MLD58_RS24305 | 43418..43669 | - | 252 | WP_001291964 | hypothetical protein | - |
| MLD58_RS24980 | 44168..44263 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| MLD58_RS24315 | 44328..44504 | - | 177 | WP_001054900 | hypothetical protein | - |
| MLD58_RS24320 | 44836..45045 | + | 210 | WP_000062602 | HEAT repeat domain-containing protein | - |
| MLD58_RS24325 | 45117..45779 | - | 663 | WP_193793429 | plasmid IncI1-type surface exclusion protein ExcA | - |
| MLD58_RS24330 | 45844..48012 | - | 2169 | WP_000698366 | DotA/TraY family protein | traY |
| MLD58_RS24335 | 48109..48693 | - | 585 | WP_001037996 | IncI1-type conjugal transfer protein TraX | - |
| MLD58_RS24340 | 48722..49924 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| MLD58_RS24345 | 49891..50505 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| MLD58_RS24350 | 50505..53549 | - | 3045 | WP_001024776 | IncI1-type conjugal transfer protein TraU | traU |
| MLD58_RS24355 | 53639..54439 | - | 801 | WP_001164792 | IncI1-type conjugal transfer protein TraT | traT |
| MLD58_RS24360 | 54423..54611 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| MLD58_RS24365 | 54675..55079 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| MLD58_RS24370 | 55130..55657 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| MLD58_RS24375 | 55657..56361 | - | 705 | WP_023155244 | IncI1-type conjugal transfer protein TraP | traP |
| MLD58_RS24380 | 56361..57650 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| MLD58_RS24385 | 57653..58636 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| MLD58_RS24390 | 58647..59339 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| MLD58_RS24395 | 59336..59683 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| MLD58_RS24400 | 59701..63468 | - | 3768 | WP_057517056 | LPD7 domain-containing protein | - |
| MLD58_RS24405 | 63558..64109 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| MLD58_RS24410 | 64124..64414 | - | 291 | WP_001299214 | hypothetical protein | traK |
| MLD58_RS24415 | 64411..65559 | - | 1149 | WP_001024976 | plasmid transfer ATPase TraJ | virB11 |
| MLD58_RS24420 | 65556..66374 | - | 819 | WP_193793431 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| MLD58_RS24425 | 66371..66829 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| MLD58_RS24430 | 67224..67808 | - | 585 | WP_000977520 | histidine phosphatase family protein | - |
| MLD58_RS24435 | 67868..69070 | - | 1203 | WP_000976357 | conjugal transfer protein TraF | - |
| MLD58_RS24440 | 69156..69980 | - | 825 | WP_057517055 | conjugal transfer protein TraE | traE |
| MLD58_RS24445 | 70131..71285 | - | 1155 | WP_001139955 | site-specific integrase | - |
| MLD58_RS25050 | 72697..72921 | + | 225 | Protein_84 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| MLD58_RS24450 | 72918..74354 | - | 1437 | WP_015058913 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| MLD58_RS24455 | 74342..74998 | - | 657 | WP_001193551 | A24 family peptidase | - |
| MLD58_RS24460 | 74983..75543 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| MLD58_RS24465 | 75553..76167 | - | 615 | WP_000908228 | type 4 pilus major pilin | - |
| MLD58_RS24470 | 76184..77269 | - | 1086 | WP_001208803 | type II secretion system F family protein | - |
| MLD58_RS24475 | 77282..78835 | - | 1554 | WP_000362204 | ATPase, T2SS/T4P/T4SS family | virB11 |
| MLD58_RS24480 | 78846..79298 | - | 453 | WP_001247333 | type IV pilus biogenesis protein PilP | - |
| MLD58_RS24485 | 79285..80580 | - | 1296 | WP_000752776 | type 4b pilus protein PilO2 | - |
| MLD58_RS24490 | 80573..82255 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| MLD58_RS24495 | 82269..82706 | - | 438 | WP_000539811 | type IV pilus biogenesis protein PilM | - |
| MLD58_RS24500 | 82706..83773 | - | 1068 | WP_021513968 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 6550 | GenBank | NZ_CP092912 |
| Plasmid name | pNDM13-SR33 | Incompatibility group | IncI1 |
| Plasmid size | 88258 bp | Coordinate of oriT [Strand] | 33954..34042 [-] |
| Host baterium | Salmonella enterica subsp. enterica strain SR33 |
Cargo genes
| Drug resistance gene | blaNDM-13 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |