Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114334 |
| Name | oriT_IncI1-I(Gamma)  |
| Organism | Salmonella enterica subsp. enterica serovar Schwarzengrund strain SEWLSH-3 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP130088 (30797..30885 [-], 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_IncI1-I(Gamma)
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9184 | GenBank | WP_011264053 |
| Name | nikB_QPE09_RS24995_IncI1-I(Gamma) |
UniProt ID | A0A767TAZ8 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103882.34 Da Isoelectric Point: 7.4198
>WP_011264053.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A767TAZ8 |
Auxiliary protein
| ID | 5378 | GenBank | WP_001283947 |
| Name | WP_001283947_IncI1-I(Gamma) |
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 | 10642 | GenBank | WP_072107381 |
| Name | trbC_QPE09_RS25000_IncI1-I(Gamma) |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86883.07 Da Isoelectric Point: 6.7712
>WP_072107381.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTAKTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTAKTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 36263..75678
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| QPE09_RS25000 (QPE09_25000) | 33979..36270 | - | 2292 | WP_072107381 | F-type conjugative transfer protein TrbC | - |
| QPE09_RS25005 (QPE09_25005) | 36263..37333 | - | 1071 | WP_000151579 | IncI1-type conjugal transfer protein TrbB | trbB |
| QPE09_RS25010 (QPE09_25010) | 37352..38560 | - | 1209 | WP_001383960 | IncI1-type conjugal transfer protein TrbA | trbA |
| QPE09_RS25015 (QPE09_25015) | 38778..39764 | - | 987 | WP_112384339 | hypothetical protein | - |
| QPE09_RS25020 (QPE09_25020) | 40037..40189 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| QPE09_RS25025 (QPE09_25025) | 40261..40512 | - | 252 | WP_001291964 | hypothetical protein | - |
| QPE09_RS25030 (QPE09_25030) | 41011..41106 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| QPE09_RS25035 (QPE09_25035) | 41171..41347 | - | 177 | WP_001054901 | hypothetical protein | - |
| QPE09_RS25040 (QPE09_25040) | 41679..41888 | + | 210 | WP_000062602 | HEAT repeat domain-containing protein | - |
| QPE09_RS25045 (QPE09_25045) | 41960..42622 | - | 663 | WP_060527638 | plasmid IncI1-type surface exclusion protein ExcA | - |
| QPE09_RS25050 (QPE09_25050) | 42693..44861 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| QPE09_RS25055 (QPE09_25055) | 44958..45542 | - | 585 | WP_060527640 | IncI1-type conjugal transfer protein TraX | - |
| QPE09_RS25060 (QPE09_25060) | 45571..46773 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| QPE09_RS25065 (QPE09_25065) | 46740..47354 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| QPE09_RS25070 (QPE09_25070) | 47354..50398 | - | 3045 | WP_071447696 | IncI1-type conjugal transfer protein TraU | traU |
| QPE09_RS25075 (QPE09_25075) | 50488..51288 | - | 801 | WP_060527642 | IncI1-type conjugal transfer protein TraT | traT |
| QPE09_RS25080 (QPE09_25080) | 51272..51460 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| QPE09_RS25085 (QPE09_25085) | 51524..51928 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| QPE09_RS25090 (QPE09_25090) | 51979..52506 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| QPE09_RS25095 (QPE09_25095) | 52506..53210 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| QPE09_RS25100 (QPE09_25100) | 53210..54499 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| QPE09_RS25105 (QPE09_25105) | 54502..55485 | - | 984 | WP_021513963 | IncI1-type conjugal transfer protein TraN | traN |
| QPE09_RS25110 (QPE09_25110) | 55496..56188 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| QPE09_RS25115 (QPE09_25115) | 56185..56532 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| QPE09_RS25120 (QPE09_25120) | 56550..60316 | - | 3767 | Protein_70 | LPD7 domain-containing protein | - |
| QPE09_RS25125 (QPE09_25125) | 60401..60952 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| QPE09_RS25130 (QPE09_25130) | 60967..61257 | - | 291 | WP_001299214 | hypothetical protein | traK |
| QPE09_RS25135 (QPE09_25135) | 61254..62402 | - | 1149 | WP_001024976 | plasmid transfer ATPase TraJ | virB11 |
| QPE09_RS25140 (QPE09_25140) | 62399..63217 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| QPE09_RS25145 (QPE09_25145) | 63214..63672 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| QPE09_RS25150 (QPE09_25150) | 64067..64651 | - | 585 | WP_000977520 | histidine phosphatase family protein | - |
| QPE09_RS25155 (QPE09_25155) | 64711..65913 | - | 1203 | WP_000976357 | conjugal transfer protein TraF | - |
| QPE09_RS25160 (QPE09_25160) | 65999..66823 | - | 825 | WP_015058912 | conjugal transfer protein TraE | traE |
| QPE09_RS25165 (QPE09_25165) | 66974..68128 | - | 1155 | WP_001139955 | tyrosine-type recombinase/integrase | - |
| QPE09_RS25170 (QPE09_25170) | 69648..69896 | + | 249 | WP_001349157 | hypothetical protein | - |
| QPE09_RS25175 (QPE09_25175) | 69893..71185 | - | 1293 | WP_039719938 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| QPE09_RS25180 (QPE09_25180) | 71185..71841 | - | 657 | WP_001193551 | A24 family peptidase | - |
| QPE09_RS25185 (QPE09_25185) | 71826..72386 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| QPE09_RS25190 (QPE09_25190) | 72396..73010 | - | 615 | WP_000908228 | type 4 pilus major pilin | - |
| QPE09_RS25195 (QPE09_25195) | 73027..74112 | - | 1086 | WP_001208803 | type II secretion system F family protein | - |
| QPE09_RS25200 (QPE09_25200) | 74125..75678 | - | 1554 | WP_000362204 | GspE/PulE family protein | virB11 |
| QPE09_RS25205 (QPE09_25205) | 75689..76141 | - | 453 | WP_001247333 | type IV pilus biogenesis protein PilP | - |
| QPE09_RS25210 (QPE09_25210) | 76128..77423 | - | 1296 | WP_000752776 | type 4b pilus protein PilO2 | - |
| QPE09_RS25215 (QPE09_25215) | 77416..79098 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| QPE09_RS25220 (QPE09_25220) | 79112..79549 | - | 438 | WP_000539811 | type IV pilus biogenesis protein PilM | - |
| QPE09_RS25225 (QPE09_25225) | 79549..80616 | - | 1068 | WP_021513968 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 14769 | GenBank | NZ_CP130088 |
| Plasmid name | IncI1-I(Gamma) | Incompatibility group | IncI1 |
| Plasmid size | 85101 bp | Coordinate of oriT [Strand] | 30797..30885 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Schwarzengrund strain SEWLSH-3 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |